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Elisey Kobzev

Doctor of Philosophy, (Biochemistry)
Study Completed: 2017
College of Sciences

Citation

Thesis Title
Molecular Dynamics Modelling of Biomolecular Interactions with Lipid Membranes and Novel Coarse Grain Lipid Model Development

Read article at Massey Research Online: MRO icon

Molecular dynamics computer simulations provide valuable opportunities to study biomolecules, such as lipid membranes and the molecules that interact with them, at near-atomic resolutions. Mr Kobzev studied novel antibacterial peptides to help research medicines which combat drug resistant bacteria. The mechanism of peptide insertion into bacterial cell membranes was investigated, key structural elements were outlined to facilitate further drug research, and the behaviour of antifreeze protein type-1 was researched. The protein was found to be flexible in solution, which contrasted with rod-like solid phase behaviour. In certain cases, two proteins aggregated together, interacting with unsaturated lipid membranes and providing insight into freezing damage prevention mechanisms. To facilitate simulation of larger biological membrane systems, a novel supra-atomic lipid modelling approach was developed. The lipid model is polarisable, unlike many current popular supra-atomic models and is intended to pave a way for the development of a 'plug and play' lipid parameter library.

Supervisors
Associate Professor Jane Allison
Distinguished Professor Peter Schwerdtfeger